Major histocompatibility complex (MHC) molecules play a central role in determining the specific viral peptides recognized by T lymphocytes. The relative lack of information on rhesus MHC molecules has limited our ability to examine the role of these molecules in determining the immune response to SIV and modulating disease progression. We have previously developed a novel set of PCR primers to amplify rhesus class I MHC cDNA. Six full length MHC clones were obtained from a single animal andtransfected into cell lines for further analysis. All of these clones appear to represent novel rhesus sequences, as none are represented in the Genebank database. Phylogenetic analysis of these sequences suggests that there are four MHC class I A molecules and two MHC class I B molecules from this animal. To identify the peptides presented by these MHC molecules, we transfected class I molecules into the T2 cell line and examined upregulation of surface class I MHC expression following incubation with peptides. Using this technique, we have identified one MHC molecule able to bind the SIV V2 peptide 12K. Additional MHC molecules were sequenced from this animal. Use of this approach should facilitate identification of the restricting alleles for SIV peptides recognized by cytotoxic T lymphocytes.